In-Depth Exploration of Human Gut Microbiota: A Review

Human Gut Microbiota Attributes

Authors

  • Maliha Rashid University Institute of Biochemistry and Biotechnology, PMAS Arid Agriculture University Rawalpindi Pakistan https://orcid.org/0000-0001-7728-5452
  • Dwaipayaan Sinha Department of Botany, Government General Degree College, Mohanpur, Paschim Medinipur, West Bengal-721436, India, https://orcid.org/0000-0001-7870-8998
  • Muhammad Usama Alpha Genomics Private Limited, Islamabad, 45710, Pakistan https://orcid.org/0000-0003-0548-5812
  • Mariam Badam Quaid-i-Azam University Islamabad-45320, Pakistan
  • Maryam Idrees Quaid-i-Azam University Islamabad-45320, Pakistan
  • Saiqa Noureen University Institute of Biochemistry and Biotechnology, PMAS Arid Agriculture University Rawalpindi-46000, Pakistan
  • Reem Nadeem Quaid-i-Azam University Islamabad-45320, Pakistan
  • Muhammad Mustajab Khan Quaid-i-Azam University Islamabad-45320, Pakistan
  • Shakira Ghazanfar National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre Islamabad-45500 https://orcid.org/0000-0002-6277-5106

Keywords:

Gut Microbiota, Neurotransmitters, GABA, Machin Learning, human gut microbiome

Abstract

Gut microbiota has a significant role in maintaining the overall health in humans and higher animals. Balanced diet, genetic makeup, and use of antibiotics highly influence the microbial population in the gastrointestinal tract. This review article presents a detailed background on the gut microbiota, including its composition and the various factors influencing its diversity and stability. Strategies for maintaining a healthy gut microbiota are explored, along with an examination of the role of neurotransmitters in regulating gut-brain communication. Research shows that machine learning has a huge potential in elucidating the gut microbiome. Wellbeing and health is directly associated with gut microbiome.

References

Abranches, J., Zeng, L., Kajfasz, J. K., Palmer, S. R., Chakraborty, B., Wen, Z. T., Richards, V. P., Brady, L. J., & Lemos, J. A. (2018). Biology of Oral Streptococci. Microbiology Spectrum, 6(5). https://doi.org/10.1128/microbiolspec.GPP3-0042-2018

Ahmed, S., Macfarlane, G. T., Fite, A., McBain, A. J., Gilbert, P., & Macfarlane, S. (2007). Mucosa-Associated Bacterial Diversity in Relation to Human Terminal Ileum and Colonic Biopsy Samples. Applied and Environmental Microbiology, 73(22), 7435–7442. https://doi.org/10.1128/AEM.01143-07

Ahn, J., & Hayes, R. B. (2021). Environmental Influences on the Human Microbiome and Implications for Noncommunicable Disease. Annual Review of Public Health, 42(1), 277–292. https://doi.org/10.1146/annurev-publhealth-012420-105020

Akimbekov, N. S., Digel, I., Sherelkhan, D. K., Lutfor, A. B., & Razzaque, M. S. (2020). Vitamin D and the Host-Gut Microbiome: A Brief Overview. ACTA HISTOCHEMICA ET CYTOCHEMICA, 53(3), 33–42. https://doi.org/10.1267/ahc.20011

Alam, M. T., Amos, G. C. A., Murphy, A. R. J., Murch, S., Wellington, E. M. H., & Arasaradnam, R. P. (2020). Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels. Gut Pathogens, 12(1), 1. https://doi.org/10.1186/s13099-019-0341-6

Aleksijević, L. H., Aleksijević, M., Škrlec, I., Šram, M., Šram, M., & Talapko, J. (2022). Porphyromonas gingivalis Virulence Factors and Clinical Significance in Periodontal Disease and Coronary Artery Diseases. Pathogens, 11(10), 1173. https://doi.org/10.3390/pathogens11101173

Alseekh, S., Aharoni, A., Brotman, Y., Contrepois, K., D’Auria, J., Ewald, J., C. Ewald, J., Fraser, P. D., Giavalisco, P., Hall, R. D., Heinemann, M., Link, H., Luo, J., Neumann, S., Nielsen, J., Perez de Souza, L., Saito, K., Sauer, U., Schroeder, F. C., … Fernie, A. R. (2021). Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices. Nature Methods, 18(7), 747–756. https://doi.org/10.1038/s41592-021-01197-1

Andersen, V., Olsen, A., Carbonnel, F., Tjønneland, A., & Vogel, U. (2012). Diet and risk of inflammatory bowel disease. Digestive and Liver Disease, 44(3), 185–194. https://doi.org/10.1016/j.dld.2011.10.001

Angermueller, C., Pärnamaa, T., Parts, L., & Stegle, O. (2016). Deep learning for computational biology. Molecular Systems Biology, 12(7). https://doi.org/10.15252/msb.20156651

Arboleya, S., Binetti, A., Salazar, N., Fernández, N., Solís, G., Hernández-Barranco, A., Margolles, A., los Reyes-Gavilán, C. G., & Gueimonde, M. (2012a). Establishment and development of intestinal microbiota in preterm neonates. FEMS Microbiology Ecology, 79(3), 763–772. https://doi.org/10.1111/j.1574-6941.2011.01261.x

Arboleya, S., Binetti, A., Salazar, N., Fernández, N., Solís, G., Hernández-Barranco, A., Margolles, A., los Reyes-Gavilán, C. G., & Gueimonde, M. (2012b). Establishment and development of intestinal microbiota in preterm neonates. FEMS Microbiology Ecology, 79(3), 763–772. https://doi.org/10.1111/j.1574-6941.2011.01261.x

Arnold, J. W., Roach, J., & Azcarate-Peril, M. A. (2016). Emerging Technologies for Gut Microbiome Research. Trends in Microbiology, 24(11), 887–901. https://doi.org/10.1016/j.tim.2016.06.008

Asano, Y., Hiramoto, T., Nishino, R., Aiba, Y., Kimura, T., Yoshihara, K., Koga, Y., & Sudo, N. (2012). Critical role of gut microbiota in the production of biologically active, free catecholamines in the gut lumen of mice. American Journal of Physiology. Gastrointestinal and Liver Physiology, 303(11). https://doi.org/10.1152/AJPGI.00341.2012

Ayechu-Muruzabal, V., van Stigt, A. H., Mank, M., Willemsen, L. E. M., Stahl, B., Garssen, J., & van’t Land, B. (2018). Diversity of Human Milk Oligosaccharides and Effects on Early Life Immune Development. Frontiers in Pediatrics, 6. https://doi.org/10.3389/fped.2018.00239

Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005). Host-bacterial mutualism in the human intestine. Science, 307(5717), 1915–1920. https://doi.org/10.1126/science.1104816

Barreau, M., Pagnier, I., & La Scola, B. (2013). Improving the identification of anaerobes in the clinical microbiology laboratory through MALDI-TOF mass spectrometry. Anaerobe, 22, 123–125. https://doi.org/10.1016/j.anaerobe.2013.04.011

Beam, A. L., & Kohane, I. S. (2018). Big Data and Machine Learning in Health Care. JAMA, 319(13), 1317. https://doi.org/10.1001/jama.2017.18391

Berg, G., Rybakova, D., Fischer, D., Cernava, T., Vergès, M.-C. C., Charles, T., Chen, X., Cocolin, L., Eversole, K., Corral, G. H., Kazou, M., Kinkel, L., Lange, L., Lima, N., Loy, A., Macklin, J. A., Maguin, E., Mauchline, T., McClure, R., … Schloter, M. (2020). Microbiome definition re-visited: old concepts and new challenges. Microbiome, 8(1), 103. https://doi.org/10.1186/s40168-020-00875-0

Berrazeg, M., Diene, S. M., Drissi, M., Kempf, M., Richet, H., Landraud, L., & Rolain, J. M. (2013). Biotyping of Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates from France and Algeria Using MALDI-TOF MS. PLoS ONE, 8(4). https://doi.org/10.1371/journal.pone.0061428

Bertrand, P. P., & Bertrand, R. L. (2010). Serotonin release and uptake in the gastrointestinal tract. Autonomic Neuroscience, 153(1–2), 47–57. https://doi.org/10.1016/J.AUTNEU.2009.08.002

Bhadra, P., Yan, J., Li, J., Fong, S., & Siu, S. W. I. (2018). AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest. Scientific Reports, 8(1), 1697. https://doi.org/10.1038/s41598-018-19752-w

Bindels, L. B., Porporato, P., Dewulf, E. M., Verrax, J., Neyrinck, A. M., Martin, J. C., Scott, K. P., Buc Calderon, P., Feron, O., Muccioli, G. G., Sonveaux, P., Cani, P. D., & Delzenne, N. M. (2012a). Gut microbiota-derived propionate reduces cancer cell proliferation in the liver. British Journal of Cancer, 107(8), 1337–1344. https://doi.org/10.1038/bjc.2012.409

Bindels, L. B., Porporato, P., Dewulf, E. M., Verrax, J., Neyrinck, A. M., Martin, J. C., Scott, K. P., Buc Calderon, P., Feron, O., Muccioli, G. G., Sonveaux, P., Cani, P. D., & Delzenne, N. M. (2012b). Gut microbiota-derived propionate reduces cancer cell proliferation in the liver. British Journal of Cancer, 107(8), 1337–1344. https://doi.org/10.1038/bjc.2012.409

Blekhman, R., Goodrich, J. K., Huang, K., Sun, Q., Bukowski, R., Bell, J. T., Spector, T. D., Keinan, A., Ley, R. E., Gevers, D., & Clark, A. G. (2015). Host genetic variation impacts microbiome composition across human body sites. Genome Biology, 16(1). https://doi.org/10.1186/S13059-015-0759-1

Borodovitsyna, O., Flamini, M., & Chandler, D. (2017). Noradrenergic Modulation of Cognition in Health and Disease. Neural Plasticity, 2017. https://doi.org/10.1155/2017/6031478

Cahana, I., & Iraqi, F. A. (2020). Impact of host genetics on gut microbiome: Take‐home lessons from human and mouse studies. Animal Models and Experimental Medicine, 3(3), 229. https://doi.org/10.1002/AME2.12134

Cai, J., Rimal, B., Jiang, C., Chiang, J. Y. L., & Patterson, A. D. (2022). Bile acid metabolism and signaling, the microbiota, and metabolic disease. Pharmacology & Therapeutics, 237, 108238. https://doi.org/10.1016/j.pharmthera.2022.108238

Callegari, E. A. (2016). Shotgun Proteomics Analysis of Estrogen Effects in the Uterus Using Two-Dimensional Liquid Chromatography and Tandem Mass Spectrometry (pp. 131–148). https://doi.org/10.1007/978-1-4939-3127-9_11

Cammarota, G., Ianiro, G., Ahern, A., Carbone, C., Temko, A., Claesson, M. J., Gasbarrini, A., & Tortora, G. (2020). Gut microbiome, big data and machine learning to promote precision medicine for cancer. Nature Reviews Gastroenterology & Hepatology, 17(10), 635–648. https://doi.org/10.1038/s41575-020-0327-3

Canani, R. B. (2011). Potential beneficial effects of butyrate in intestinal and extraintestinal diseases. World Journal of Gastroenterology, 17(12), 1519. https://doi.org/10.3748/wjg.v17.i12.1519

Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C. A., Turnbaugh, P. J., Fierer, N., & Knight, R. (2011). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences, 108(supplement_1), 4516–4522. https://doi.org/10.1073/pnas.1000080107

Carey, C. M., Kirk, J. L., Ojha, S., & Kostrzynska, M. (2007). Current and future uses of real-time polymerase chain reaction and microarrays in the study of intestinal microbiota, and probiotic use and effectiveness. Canadian Journal of Microbiology, 53(5), 537–550. https://doi.org/10.1139/W07-039

Carpaij, N., Willems, R. J. L., Bonten, M. J. M., & Fluit, A. C. (2011). Comparison of the identification of coagulase-negative staphylococci by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and tuf sequencing. European Journal of Clinical Microbiology and Infectious Diseases, 30(10), 1169–1172. https://doi.org/10.1007/s10096-011-1204-3

Casimiro-Soriguer, C. S., Loucera, C., Peña-Chilet, M., & Dopazo, J. (2022). Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer. Scientific Reports, 12(1), 450. https://doi.org/10.1038/s41598-021-04182-y

Cavalier-Smith, T., Brasier, M., & Embley, T. M. (2006). Introduction: how and when did microbes change the world? Philosophical Transactions of the Royal Society B: Biological Sciences, 361(1470), 845–850. https://doi.org/10.1098/rstb.2006.1847

Chassaing, B., & Gewirtz, A. T. (2014). Gut Microbiota, Low-grade Inflammation, and Metabolic Syndrome. Toxicologic Pathology, 42(1), 49–53. https://doi.org/10.1177/0192623313508481

Chen, Y., Xu, J., & Chen, Y. (2021a). Regulation of Neurotransmitters by the Gut Microbiota and Effects on Cognition in Neurological Disorders. Nutrients, 13(6). https://doi.org/10.3390/NU13062099

Chen, Y., Xu, J., & Chen, Y. (2021b). Regulation of Neurotransmitters by the Gut Microbiota and Effects on Cognition in Neurological Disorders. Nutrients, 13(6). https://doi.org/10.3390/NU13062099

Chen, Y., Zhou, J., & Wang, L. (2021). Role and Mechanism of Gut Microbiota in Human Disease. Frontiers in Cellular and Infection Microbiology, 11(March), 1–12. https://doi.org/10.3389/fcimb.2021.625913

Cheng, H.-Y., Ning, M.-X., Chen, D.-K., & Ma, W.-T. (2019). Interactions Between the Gut Microbiota and the Host Innate Immune Response Against Pathogens. Frontiers in Immunology, 10. https://doi.org/10.3389/fimmu.2019.00607

Chistoserdova, L. (2010). Recent progress and new challenges in metagenomics for biotechnology. Biotechnology Letters, 32(10), 1351–1359. https://doi.org/10.1007/s10529-010-0306-9

Choo, J. M., Kanno, T., Zain, N. M. M., Leong, L. E. X., Abell, G. C. J., Keeble, J. E., Bruce, K. D., Mason, A. J., & Rogers, G. B. (2017). Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions. MSphere, 2(1). https://doi.org/10.1128/mSphere.00005-17

Clark, C. G., Kruczkiewicz, P., Guan, C., McCorrister, S. J., Chong, P., Wylie, J., van Caeseele, P., Tabor, H. A., Snarr, P., Gilmour, M. W., Taboada, E. N., & Westmacott, G. R. (2013). Evaluation of MALDI-TOF mass spectroscopy methods for determination of Escherichia coli pathotypes. Journal of Microbiological Methods, 94(3), 180–191. https://doi.org/10.1016/j.mimet.2013.06.020

Coelho, G. D. P., Ayres, L. F. A., Barreto, D. S., Henriques, B. D., Prado, M. R. M. C., & Passos, C. M. Dos. (2021). Acquisition of microbiota according to the type of birth: an integrative review. Revista Latino-Americana de Enfermagem, 29. https://doi.org/10.1590/1518.8345.4466.3446

Collins, S. L., & Patterson, A. D. (2020). The gut microbiome: an orchestrator of xenobiotic metabolism. Acta Pharmaceutica Sinica B, 10(1), 19–32. https://doi.org/10.1016/j.apsb.2019.12.001

Cooke, G., Behan, J., Clarke, N., Gorman, W., & Costello, M. (2005). Comparing the gut flora of Irish breastfed and formula-fed neonates aged between birth and 6 weeks old. Microbial Ecology in Health and Disease, 17(3), 163–168. https://doi.org/10.1080/08910600500430664

Cooper, K. K., & Songer, J. G. (2009). Necrotic enteritis in chickens: A paradigm of enteric infection by Clostridium perfringens type A. Anaerobe, 15(1–2), 55–60. https://doi.org/10.1016/j.anaerobe.2009.01.006

Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., & Knight, R. (2009). Bacterial Community Variation in Human Body Habitats Across Space and Time. Science, 326(5960), 1694–1697. https://doi.org/10.1126/science.1177486

Cryan, J. F., O’Riordan, K. J., Sandhu, K., Peterson, V., & Dinan, T. G. (2020). The gut microbiome in neurological disorders. The Lancet Neurology, 19(2), 179–194. https://doi.org/10.1016/S1474-4422(19)30356-4

Czosnykowska-Łukacka, Orczyk-Pawiłowicz, Broers, & Królak-Olejnik. (2019). Lactoferrin in Human Milk of Prolonged Lactation. Nutrients, 11(10), 2350. https://doi.org/10.3390/nu11102350

D’Amelio, P., & Sassi, F. (2018). Gut Microbiota, Immune System, and Bone. Calcified Tissue International, 102(4), 415–425. https://doi.org/10.1007/S00223-017-0331-Y

D’Argenio, V., Casaburi, G., Precone, V., Pagliuca, C., Colicchio, R., Sarnataro, D., Discepolo, V., Kim, S. M., Russo, I., Del Vecchio Blanco, G., Horner, D. S., Chiara, M., Pesole, G., Salvatore, P., Monteleone, G., Ciacci, C., Caporaso, G. J., Jabrì, B., Salvatore, F., & Sacchetti, L. (2016). Metagenomics Reveals Dysbiosis and a Potentially Pathogenic N. flavescens Strain in Duodenum of Adult Celiac Patients. American Journal of Gastroenterology, 111(6), 879–890. https://doi.org/10.1038/ajg.2016.95

DC, S. (2001). Microbial biota of the human intestine: a tribute to some pioneering scientists. Curr Issues Intest Microbiol., 1–15.

Degand, N., Carbonnelle, E., Dauphin, B., Beretti, J. L., Le Bourgeois, M., Sermet-Gaudelus, I., Segonds, C., Berche, P., Nassif, X., & Ferroni, A. (2008). Matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis patients. Journal of Clinical Microbiology, 46(10), 3361–3367. https://doi.org/10.1128/JCM.00569-08

Della Vecchia, A., Arone, A., Piccinni, A., Mucci, F., & Marazziti, D. (2022). GABA System in Depression: Impact on Pathophysiology and Psychopharmacology. Current Medicinal Chemistry, 29(36), 5710–5730. https://doi.org/10.2174/0929867328666211115124149

Di Pilato, V., Freschi, G., Ringressi, M. N., Pallecchi, L., Rossolini, G. M., & Bechi, P. (2016). The esophageal microbiota in health and disease. Annals of the New York Academy of Sciences, 1381(1), 21–33. https://doi.org/10.1111/nyas.13127

Dicks, L. M. T. (2022). Gut Bacteria and Neurotransmitters. Microorganisms, 10(9). https://doi.org/10.3390/MICROORGANISMS10091838

Dicks, L. M. T., Hurn, D., & Hermanus, D. (2021). Gut bacteria and neuropsychiatric disorders. Microorganisms, 9(12). https://doi.org/10.3390/MICROORGANISMS9122583

Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences, 107(26), 11971–11975. https://doi.org/10.1073/pnas.1002601107

Dong, L.-N., Wang, M., Guo, J., & Wang, J.-P. (2019). Role of intestinal microbiota and metabolites in inflammatory bowel disease. Chinese Medical Journal, 132(13), 1610–1614. https://doi.org/10.1097/CM9.0000000000000290

Dridi, B., Raoult, D., & Drancourt, M. (2012). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of Archaea: Towards the universal identification of living organisms. Apmis, 120(2), 85–91. https://doi.org/10.1111/j.1600-0463.2011.02833.x

Dupont, C., Sivadon-Tardy, V., Bille, E., Dauphin, B., Beretti, J. L., Alvarez, A. S., Degand, N., Ferroni, A., Rottman, M., Herrmann, J. L., Nassif, X., Ronco, E., & Carbonnelle, E. (2010). Identification of clinical coagulase-negative staphylococci, isolated in microbiology laboratories, by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and two automated systems. Clinical Microbiology and Infection, 16(7), 998–1004. https://doi.org/10.1111/j.1469-0691.2009.03036.x

Duranti, S., Ruiz, L., Lugli, G. A., Tames, H., Milani, C., Mancabelli, L., Mancino, W., Longhi, G., Carnevali, L., Sgoifo, A., Margolles, A., Ventura, M., Ruas-Madiedo, P., & Turroni, F. (2020). Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA. Scientific Reports, 10(1), 14112. https://doi.org/10.1038/s41598-020-70986-z

Elsalem, L., Jum’ah, A. A., Alfaqih, M. A., & Aloudat, O. (2020). The Bacterial Microbiota of Gastrointestinal Cancers: Role in Cancer Pathogenesis and Therapeutic Perspectives. Clinical and Experimental Gastroenterology, 13, 151–185. https://doi.org/10.2147/CEG.S243337

Eribe, E. R. K., & Olsen, I. (2017). Leptotrichia species in human infections II. Journal of Oral Microbiology, 9(1), 1368848. https://doi.org/10.1080/20002297.2017.1368848

Esberg, A., Barone, A., Eriksson, L., Lif Holgerson, P., Teneberg, S., & Johansson, I. (2020). Corynebacterium matruchotii Demography and Adhesion Determinants in the Oral Cavity of Healthy Individuals. Microorganisms, 8(11), 1780. https://doi.org/10.3390/microorganisms8111780

Fassarella, M., Blaak, E. E., Penders, J., Nauta, A., Smidt, H., & Zoetendal, E. G. (2021). Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health. Gut, 70(3), 595–605. https://doi.org/10.1136/GUTJNL-2020-321747

Faust, K., & Raes, J. (2012). Microbial interactions: From networks to models. Nature Reviews Microbiology, 10(8), 538–550. https://doi.org/10.1038/nrmicro2832

Feng, X. wei, Ding, W. ping, Xiong, L. yun, Guo, L., Sun, J. ming, & Xiao, P. (2018). Recent Advancements in Intestinal Microbiota Analyses: A Review for Non-Microbiologists. Current Medical Science, 38(6), 949–961. https://doi.org/10.1007/s11596-018-1969-z

Fischer, S. G., & Lerman, L. S. (1980). Separation of random fragments of DNA according to properties of their sequences. Proceedings of the National Academy of Sciences of the United States of America, 77(8), 4420–4424. https://doi.org/10.1073/pnas.77.8.4420

Flint, H. J., Scott, K. P., Louis, P., & Duncan, S. H. (2012). The role of the gut microbiota in nutrition and health. Nature Reviews Gastroenterology & Hepatology, 9(10), 577–589. https://doi.org/10.1038/nrgastro.2012.156

Franzosa, E. A., Morgan, X. C., Segata, N., Waldron, L., Reyes, J., Earl, A. M., Giannoukos, G., Boylan, M. R., Ciulla, D., Gevers, D., Izard, J., Garrett, W. S., Chan, A. T., & Huttenhower, C. (2014). Relating the metatranscriptome and metagenome of the human gut. Proceedings of the National Academy of Sciences of the United States of America, 111(22). https://doi.org/10.1073/pnas.1319284111

Fukui, A., Takagi, T., Naito, Y., Inoue, R., Kashiwagi, S., Mizushima, K., Inada, Y., Inoue, K., Harusato, A., Dohi, O., Okayama, T., Katada, K., Kamada, K., Uchiyama, K., Ishikawa, T., Handa, O., Itoh, Y., & Nakagawa, M. (2020). Higher Levels of <b><i>Streptococcus</i></b> in Upper Gastrointestinal Mucosa Associated with Symptoms in Patients with Functional Dyspepsia. Digestion, 101(1), 38–45. https://doi.org/10.1159/000504090

Gabrielli, O., Zampini, L., Galeazzi, T., Padella, L., Santoro, L., Peila, C., Giuliani, F., Bertino, E., Fabris, C., & Coppa, G. V. (2011). Preterm Milk Oligosaccharides During the First Month of Lactation. Pediatrics, 128(6), e1520–e1531. https://doi.org/10.1542/peds.2011-1206

Gao, L., Xu, T., Huang, G., Jiang, S., Gu, Y., & Chen, F. (2018). Oral microbiomes: more and more importance in oral cavity and whole body. Protein & Cell, 9(5), 488–500. https://doi.org/10.1007/s13238-018-0548-1

Ghosh, A., Borst, L., Stauffer, S. H., Suyemoto, M., Moisan, P., Zurek, L., & Gookin, J. L. (2013). Mortality in Kittens Is Associated with a Shift in Ileum Mucosa-Associated Enterococci from Enterococcus hirae to Biofilm-Forming Enterococcus faecalis and Adherent Escherichia coli. Journal of Clinical Microbiology, 51(11), 3567–3578. https://doi.org/10.1128/JCM.00481-13

Gibbons, S. M., & Gilbert, J. A. (2015). Microbial diversity — exploration of natural ecosystems and microbiomes. Current Opinion in Genetics & Development, 35, 66–72. https://doi.org/10.1016/j.gde.2015.10.003

Gill, P. A., van Zelm, M. C., Muir, J. G., & Gibson, P. R. (2018). Review article: short chain fatty acids as potential therapeutic agents in human gastrointestinal and inflammatory disorders. Alimentary Pharmacology & Therapeutics, 48(1), 15–34. https://doi.org/10.1111/apt.14689

Gill, S. R., Pop, M., DeBoy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., Gordon, J. I., Relman, D. A., Fraser-Liggett, C. M., & Nelson, K. E. (2006). Metagenomic Analysis of the Human Distal Gut Microbiomer10.1126/science.1124234. Science, 312(5778), 1355–1359.

Glassner, K. L., Abraham, B. P., & Quigley, E. M. M. (2020). The microbiome and inflammatory bowel disease. The Journal of Allergy and Clinical Immunology, 145(1), 16–27. https://doi.org/10.1016/J.JACI.2019.11.003

Gomaa, E. Z. (2020). Human gut microbiota/microbiome in health and diseases: a review. Antonie van Leeuwenhoek, 113(12), 2019–2040. https://doi.org/10.1007/S10482-020-01474-7

Gong, D., Gong, X., Wang, L., Yu, X., & Dong, Q. (2016). Involvement of Reduced Microbial Diversity in Inflammatory Bowel Disease. Gastroenterology Research and Practice, 2016, 1–7. https://doi.org/10.1155/2016/6951091

Gou, W., Ling, C., He, Y., Jiang, Z., Fu, Y., Xu, F., Miao, Z., Sun, T., Lin, J., Zhu, H., Zhou, H., Chen, Y., & Zheng, J.-S. (2021). Interpretable Machine Learning Framework Reveals Robust Gut Microbiome Features Associated With Type 2 Diabetes. Diabetes Care, 44(2), 358–366. https://doi.org/10.2337/dc20-1536

Greve, D., Moter, A., Kleinschmidt, M. C., Pfäfflin, F., Stegemann, M. S., Kursawe, L., Grubitzsch, H., Falk, V., & Kikhney, J. (2021). Rothia aeria and Rothia dentocariosa as biofilm builders in infective endocarditis. International Journal of Medical Microbiology, 311(2), 151478. https://doi.org/10.1016/j.ijmm.2021.151478

Grice, E. A., & Segre, J. A. (2012). The human microbiome: Our second genome. Annual Review of Genomics and Human Genetics, 13(May), 151–170. https://doi.org/10.1146/annurev-genom-090711-163814

Gueimonde, M., Laitinen, K., Salminen, S., & Isolauri, E. (2007). Breast Milk: A Source of Bifidobacteria for Infant Gut Development and Maturation? Neonatology, 92(1), 64–66. https://doi.org/10.1159/000100088

Haak, B. W., Lankelma, J. M., Hugenholtz, F., Belzer, C., de Vos, W. M., & Wiersinga, W. J. (2019). Long-term impact of oral vancomycin, ciprofloxacin and metronidazole on the gut microbiota in healthy humans. Journal of Antimicrobial Chemotherapy, 74(3), 782–786. https://doi.org/10.1093/jac/dky471

Heaney, L. M. (2020). Applying mass spectrometry-based assays to explore gut microbial metabolism and associations with disease. Clinical Chemistry and Laboratory Medicine (CCLM), 58(5), 719–732. https://doi.org/10.1515/cclm-2019-0974

Hedberg, M. E., Israelsson, A., Moore, E. R. B., Svensson-Stadler, L., Wai, S. N., Pietz, G., Sandström, O., Hernell, O., Hammarström, M.-L., & Hammarström, S. (2013). Prevotella jejuni sp. nov., isolated from the small intestine of a child with coeliac disease. International Journal of Systematic and Evolutionary Microbiology, 63(Pt_11), 4218–4223. https://doi.org/10.1099/ijs.0.052647-0

Hepsomali, P., Groeger, J. A., Nishihira, J., & Scholey, A. (2020). Effects of Oral Gamma-Aminobutyric Acid (GABA) Administration on Stress and Sleep in Humans: A Systematic Review. Frontiers in Neuroscience, 14. https://doi.org/10.3389/FNINS.2020.00923

Hernández, Canfora, Jocken, & Blaak. (2019). The Short-Chain Fatty Acid Acetate in Body Weight Control and Insulin Sensitivity. Nutrients, 11(8), 1943. https://doi.org/10.3390/nu11081943

Hollister, E. B., Gao, C., & Versalovic, J. (2014). Compositional and Functional Features of the Gastrointestinal Microbiome and Their Effects on Human Health. Gastroenterology, 146(6), 1449–1458. https://doi.org/10.1053/j.gastro.2014.01.052

Horiuchi, Y., Kimura, R., Kato, N., Fujii, T., Seki, M., Endo, T., Kato, T., & Kawashima, K. (2003). Evolutional study on acetylcholine expression. Life Sciences, 72(15), 1745–1756. https://doi.org/10.1016/S0024-3205(02)02478-5

Hou, K., Wu, Z.-X., Chen, X.-Y., Wang, J.-Q., Zhang, D., Xiao, C., Zhu, D., Koya, J. B., Wei, L., Li, J., & Chen, Z.-S. (2022). Microbiota in health and diseases. Signal Transduction and Targeted Therapy, 7(1), 135. https://doi.org/10.1038/s41392-022-00974-4

Hrncir, T. (2022). Gut Microbiota Dysbiosis: Triggers, Consequences, Diagnostic and Therapeutic Options. Microorganisms, 10(3), 578. https://doi.org/10.3390/microorganisms10030578

Iatcu, C. O., Steen, A., & Covasa, M. (2021). Gut Microbiota and Complications of Type-2 Diabetes. Nutrients, 14(1), 166. https://doi.org/10.3390/nu14010166

Ingber, D. E. (2016). Reverse Engineering Human Pathophysiology with Organs-on-Chips. Cell, 164(6), 1105–1109. https://doi.org/10.1016/j.cell.2016.02.049

Janda, J. M., & Abbott, S. L. (2007). 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: Pluses, perils, and pitfalls. Journal of Clinical Microbiology, 45(9), 2761–2764. https://doi.org/10.1128/JCM.01228-07

Ji, X., Zhou, F., Zhang, Y., Deng, R., Xu, W., Bai, M., Liu, Y., Shao, L., Wang, X., & Zhou, L. (2018). Butyrate stimulates hepatic gluconeogenesis in mouse primary hepatocytes. Experimental and Therapeutic Medicine. https://doi.org/10.3892/etm.2018.7136

Johnson, A., & Loftus, E. (2021). Obesity in inflammatory bowel disease: A review of its role in the pathogenesis, natural history, and treatment of IBD. Saudi Journal of Gastroenterology, 27(4), 183. https://doi.org/10.4103/sjg.sjg_30_21

Jones, L. A., Sun, E. W., Martin, A. M., & Keating, D. J. (2020). The ever-changing roles of serotonin. The International Journal of Biochemistry & Cell Biology, 125. https://doi.org/10.1016/J.BIOCEL.2020.105776

Jung, D., Seo, E. Y., Epstein, S. S., Joung, Y., Han, J., Parfenova, V. V., Belykh, O. I., Gladkikh, A. S., & Ahn, T. S. (2014). Application of a new cultivation technology, I-tip, for studying microbial diversity in freshwater sponges of Lake Baikal, Russia. FEMS Microbiology Ecology, 90(2), 417–423. https://doi.org/10.1111/1574-6941.12399

Kerckhoffs, A. P., Samsom, M., Rest, M. E. van der, Vogel, J. de, Knol, J., Ben-Amor, K., & Akkermans, L. M. (2009). Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients. World Journal of Gastroenterology, 15(23), 2887. https://doi.org/10.3748/wjg.15.2887

Kieler, I. N., Mølbak, L., Hansen, L. L., Hermann-Bank, M. L., & Bjornvad, C. R. (2016a). Overweight and the feline gut microbiome - a pilot study. Journal of Animal Physiology and Animal Nutrition, 100(3), 478–484. https://doi.org/10.1111/jpn.12409

Kieler, I. N., Mølbak, L., Hansen, L. L., Hermann-Bank, M. L., & Bjornvad, C. R. (2016b). Overweight and the feline gut microbiome - a pilot study. Journal of Animal Physiology and Animal Nutrition, 100(3), 478–484. https://doi.org/10.1111/JPN.12409

King, C. H., Desai, H., Sylvetsky, A. C., LoTempio, J., Ayanyan, S., Carrie, J., Crandall, K. A., Fochtman, B. C., Gasparyan, L., Gulzar, N., Howell, P., Issa, N., Krampis, K., Mishra, L., Morizono, H., Pisegna, J. R., Rao, S., Ren, Y., Simonyan, V., … Mazumder, R. (2019). Baseline human gut microbiota profile in healthy people and standard reporting template. PLOS ONE, 14(9), e0206484. https://doi.org/10.1371/journal.pone.0206484

Knapp, S., Brodal, C., Peterson, J., Qi, F., Kreth, J., & Merritt, J. (2017). Natural Competence Is Common among Clinical Isolates of Veillonella parvula and Is Useful for Genetic Manipulation of This Key Member of the Oral Microbiome. Frontiers in Cellular and Infection Microbiology, 7. https://doi.org/10.3389/fcimb.2017.00139

Kuhns, M., Zautner, A. E., Rabsch, W., Zimmermann, O., Weig, M., Bader, O., & Groß, U. (2012). Rapid discrimination of Salmonella enterica serovar typhi from other serovars by MALDI-TOF mass spectrometry. PLoS ONE, 7(6), 1–6. https://doi.org/10.1371/journal.pone.0040004

La Scola, B., Fournier, P. E., & Raoult, D. (2011). Burden of emerging anaerobes in the MALDI-TOF and 16S rRNA gene sequencing era. Anaerobe, 17(3), 106–112. https://doi.org/10.1016/j.anaerobe.2011.05.010

Lagier, J. C., Armougom, F., Million, M., Hugon, P., Pagnier, I., Robert, C., Bittar, F., Fournous, G., Gimenez, G., Maraninchi, M., Trape, J. F., Koonin, E. V., La Scola, B., & Raoult, D. (2012). Microbial culturomics: Paradigm shift in the human gut microbiome study. Clinical Microbiology and Infection, 18(12), 1185–1193. https://doi.org/10.1111/1469-0691.12023

Lagier, J. C., Dubourg, G., Million, M., Cadoret, F., Bilen, M., Fenollar, F., Levasseur, A., Rolain, J. M., Fournier, P. E., & Raoult, D. (2018). Culturing the human microbiota and culturomics. Nature Reviews Microbiology, 16(9), 540–550. https://doi.org/10.1038/s41579-018-0041-0

Lagier, J.-C., Hugon, P., Khelaifia, S., Fournier, P.-E., La Scola, B., & Raoult, D. (2015). The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota. Clinical Microbiology Reviews, 28(1), 237–264. https://doi.org/10.1128/CMR.00014-14

Lange, K., Buerger, M., Stallmach, A., & Bruns, T. (2016). Effects of Antibiotics on Gut Microbiota. Digestive Diseases (Basel, Switzerland), 34(3), 260–268. https://doi.org/10.1159/000443360

La-ongkham, O., Nakphaichit, M., Nakayama, J., Keawsompong, S., & Nitisinprasert, S. (2020). Age-related changes in the gut microbiota and the core gut microbiome of healthy Thai humans. 3 Biotech, 10(6). https://doi.org/10.1007/S13205-020-02265-7

Lauber, C. L., Zhou, N., Gordon, J. I., Knight, R., & Fierer, N. (2010). Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiology Letters, 307(1), 80–86. https://doi.org/10.1111/j.1574-6968.2010.01965.x

Lee, S. A., Lim, J. Y., Kim, B.-S., Cho, S. J., Kim, N. Y., Kim, O. Bin, & Kim, Y. (2015). Comparison of the gut microbiota profile in breast-fed and formula-fed Korean infants using pyrosequencing. Nutrition Research and Practice, 9(3), 242. https://doi.org/10.4162/nrp.2015.9.3.242

Lee, S.-Y., Lee, E., Park, Y. M., & Hong, S.-J. (2018). Microbiome in the Gut-Skin Axis in Atopic Dermatitis. Allergy, Asthma & Immunology Research, 10(4), 354. https://doi.org/10.4168/aair.2018.10.4.354

Leeming, E. R., Johnson, A. J., Spector, T. D., & Roy, C. I. L. (2019). Effect of diet on the gut microbiota: Rethinking intervention duration. Nutrients, 11(12). https://doi.org/10.3390/NU11122862

Lees, E. A., Miyajima, F., Pirmohamed, M., & Carrol, E. D. (2016). The role of Clostridium difficile in the paediatric and neonatal gut — a narrative review. European Journal of Clinical Microbiology & Infectious Diseases, 35(7), 1047–1057. https://doi.org/10.1007/s10096-016-2639-3

Li, F., Hullar, M. A. J., & Lampe, J. W. (2007). Optimization of terminal restriction fragment polymorphism (TRFLP) analysis of human gut microbiota. Journal of Microbiological Methods, 68(2), 303–311. https://doi.org/10.1016/j.mimet.2006.09.006

Li, G., Yang, M., Zhou, K., Zhang, L., Tian, L., Lv, S., Jin, Y., Qian, W., Xiong, H., Lin, R., Fu, Y., & Hou, X. (2015). Diversity of Duodenal and Rectal Microbiota in Biopsy Tissues and Luminal Contents in Healthy Volunteers. Journal of Microbiology and Biotechnology, 25(7), 1136–1145. https://doi.org/10.4014/jmb.1412.12047

Li, J. J., Zhu, M., Kashyap, P. C., Chia, N., Tran, N. H., McWilliams, R. R., Bekaii-Saab, T. S., & Ma, W. W. (2021). The role of microbiome in pancreatic cancer. Cancer Metastasis Reviews, 40(3), 777–789. https://doi.org/10.1007/S10555-021-09982-2

Li, J., Zhao, F., Wang, Y., Chen, J., Tao, J., Tian, G., Wu, S., Liu, W., Cui, Q., Geng, B., Zhang, W., Weldon, R., Auguste, K., Yang, L., Liu, X., Chen, L., Yang, X., Zhu, B., & Cai, J. (2017). Gut microbiota dysbiosis contributes to the development of hypertension. Microbiome, 5(1), 14. https://doi.org/10.1186/s40168-016-0222-x

Liébana-García, R., Olivares, M., Bullich-Vilarrubias, C., López-Almela, I., Romaní-Pérez, M., & Sanz, Y. (2021). The gut microbiota as a versatile immunomodulator in obesity and associated metabolic disorders. Best Practice & Research Clinical Endocrinology & Metabolism, 35(3), 101542. https://doi.org/10.1016/j.beem.2021.101542

Lin, E., & Lane, H.-Y. (2017). Machine learning and systems genomics approaches for multi-omics data. Biomarker Research, 5(1), 2. https://doi.org/10.1186/s40364-017-0082-y

Liu, P., Wang, Y., Yang, G., Zhang, Q., Meng, L., Xin, Y., & Jiang, X. (2021). The role of short-chain fatty acids in intestinal barrier function, inflammation, oxidative stress, and colonic carcinogenesis. Pharmacological Research, 165, 105420. https://doi.org/10.1016/j.phrs.2021.105420

Liu, T., Feenstra, K. A., Heringa, J., & Huang, Z. (2020a). Influence of Gut Microbiota on Mental Health via Neurotransmitters: A Review. Journal of Artificial Intelligence for Medical Sciences, 1(1–2), 1–14. https://doi.org/10.2991/JAIMS.D.200420.001

Liu, T., Feenstra, K. A., Heringa, J., & Huang, Z. (2020b). Influence of Gut Microbiota on Mental Health via Neurotransmitters: A Review. Journal of Artificial Intelligence for Medical Sciences, 1(1–2), 1–14. https://doi.org/10.2991/JAIMS.D.200420.001

Liu, T., & Huang, Z. (2019). Evidence-based analysis of neurotransmitter modulation by gut microbiota. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 11837 LNCS, 238–249. https://doi.org/10.1007/978-3-030-32962-4_22/COVER

Long, S. L., Gahan, C. G. M., & Joyce, S. A. (2017). Interactions between gut bacteria and bile in health and disease. Molecular Aspects of Medicine, 56, 54–65. https://doi.org/10.1016/j.mam.2017.06.002

Long, S., Yang, Y., Shen, C., Wang, Y., Deng, A., Qin, Q., & Qiao, L. (2020). Metaproteomics characterizes human gut microbiome function in colorectal cancer. Npj Biofilms and Microbiomes, 6(1), 14. https://doi.org/10.1038/s41522-020-0123-4

Lowe, R., Shirley, N., Bleackley, M., Dolan, S., & Shafee, T. (2017). Transcriptomics technologies. PLOS Computational Biology, 13(5), e1005457. https://doi.org/10.1371/journal.pcbi.1005457

Łubiech, K., & Twarużek, M. (2020). Lactobacillus Bacteria in Breast Milk. Nutrients, 12(12), 3783. https://doi.org/10.3390/nu12123783

Lukumbuzya, M., Schmid, M., Pjevac, P., & Daims, H. (2019). A multicolor fluorescence in situ hybridization approach using an extended set of fluorophores to visualize microorganisms. Frontiers in Microbiology, 10(JUN), 1–13. https://doi.org/10.3389/fmicb.2019.01383

Maier, E., Anderson, R., & Roy, N. (2014). Understanding How Commensal Obligate Anaerobic Bacteria Regulate Immune Functions in the Large Intestine. Nutrients, 7(1), 45–73. https://doi.org/10.3390/nu7010045

Mailhe, M., Ricaboni, D., Vitton, V., Fournier, P.-E., Khelaifia, S., & Raoult, D. (2016). ‘ Bacteroides mediterraneensis ’ sp. nov., a new human-associated bacterium isolated from ileum specimen. New Microbes and New Infections, 13, 48–50. https://doi.org/10.1016/j.nmni.2016.06.003

Manandhar, I., Alimadadi, A., Aryal, S., Munroe, P. B., Joe, B., & Cheng, X. (2021). Gut microbiome-based supervised machine learning for clinical diagnosis of inflammatory bowel diseases. American Journal of Physiology-Gastrointestinal and Liver Physiology, 320(3), G328–G337. https://doi.org/10.1152/ajpgi.00360.2020

Marchesi, J. R., & Ravel, J. (2015). The vocabulary of microbiome research: a proposal. Microbiome, 3(1), 31. https://doi.org/10.1186/s40168-015-0094-5

Martinez-Guryn, K., Leone, V., & Chang, E. B. (2019). Regional Diversity of the Gastrointestinal Microbiome. Cell Host & Microbe, 26(3), 314–324. https://doi.org/10.1016/j.chom.2019.08.011

Mastromarino, P., Capobianco, D., Campagna, G., Laforgia, N., Drimaco, P., Dileone, A., & Baldassarre, M. E. (2014). Correlation between lactoferrin and beneficial microbiota in breast milk and infant’s feces. BioMetals, 27(5), 1077–1086. https://doi.org/10.1007/s10534-014-9762-3

Matsuoka, K., & Kanai, T. (2015). The gut microbiota and inflammatory bowel disease. Seminars in Immunopathology, 37(1), 47–55. https://doi.org/10.1007/s00281-014-0454-4

McCoubrey, L. E., Elbadawi, M., Orlu, M., Gaisford, S., & Basit, A. W. (2021). Machine Learning Uncovers Adverse Drug Effects on Intestinal Bacteria. Pharmaceutics, 13(7), 1026. https://doi.org/10.3390/pharmaceutics13071026

McOrist, A. L., Warhurst, M., McOrist, S., & Bird, A. R. (2001). Colonic Infection by Bilophila wadsworthia in Pigs. Journal of Clinical Microbiology, 39(4), 1577–1579. https://doi.org/10.1128/JCM.39.4.1577-1579.2001

Menees, S., & Chey, W. (2018). The gut microbiome and irritable bowel syndrome. F1000Research, 7, 1029. https://doi.org/10.12688/f1000research.14592.1

Meng, C., Bai, C., Brown, T. D., Hood, L. E., & Tian, Q. (2018). Human Gut Microbiota and Gastrointestinal Cancer. Genomics, Proteomics & Bioinformatics, 16(1), 33–49. https://doi.org/10.1016/J.GPB.2017.06.002

Mitev, K., & Taleski, V. (2019). Association between the Gut Microbiota and Obesity. Open Access Macedonian Journal of Medical Sciences, 7(12), 2050–2056. https://doi.org/10.3889/oamjms.2019.586

Mladenova, I. (2021). Clinical Relevance of Helicobacter pylori Infection. Journal of Clinical Medicine, 10(16), 3473. https://doi.org/10.3390/jcm10163473

Möhler, H. (2012). The GABA system in anxiety and depression and its therapeutic potential. Neuropharmacology, 62(1), 42–53. https://doi.org/10.1016/J.NEUROPHARM.2011.08.040

Moore, R. E., & Townsend, S. D. (2019). Temporal development of the infant gut microbiome. Open Biology, 9(9), 190128. https://doi.org/10.1098/rsob.190128

Morilak, D. A., Barrera, G., Echevarria, D. J., Garcia, A. S., Hernandez, A., Ma, S., & Petre, C. O. (2005). Role of brain norepinephrine in the behavioral response to stress. Progress in Neuro-Psychopharmacology & Biological Psychiatry, 29(8), 1214–1224. https://doi.org/10.1016/J.PNPBP.2005.08.007

Mou, Z., Yang, Y., Hall, A. B., & Jiang, X. (2021). The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome. BMC Genomics, 22(1), 1–11. https://doi.org/10.1186/S12864-021-08004-3/FIGURES/3

Mousavi, R., Mottawea, W., Audet, M.-C., & Hammami, R. (2022). Survival and Interplay of γ-Aminobutyric Acid-Producing Psychobiotic Candidates with the Gut Microbiota in a Continuous Model of the Human Colon. Biology, 11(9), 1311. https://doi.org/10.3390/biology11091311

Mu, C., & Zhu, W. (2019). Antibiotic effects on gut microbiota, metabolism, and beyond. Applied Microbiology and Biotechnology, 103(23–24), 9277–9285. https://doi.org/10.1007/S00253-019-10165-X

Nanjappa, S., Shah, S., & Pabbathi, S. (2015). Clostridium septicum Gas Gangrene in Colon Cancer: Importance of Early Diagnosis. Case Reports in Infectious Diseases, 2015, 1–3. https://doi.org/10.1155/2015/694247

Nechvatal, J. M., Ram, J. L., Basson, M. D., Namprachan, P., Niec, S. R., Badsha, K. Z., Matherly, L. H., Majumdar, A. P. N., & Kato, I. (2008). Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces. Journal of Microbiological Methods, 72(2), 124–132. https://doi.org/10.1016/j.mimet.2007.11.007

Niaz, B., Saeed, F., Ahmed, A., Imran, M., Maan, A. A., Khan, M. K. I., Tufail, T., Anjum, F. M., Hussain, S., & Suleria, H. A. R. (2019). Lactoferrin (LF): a natural antimicrobial protein. International Journal of Food Properties, 22(1), 1626–1641. https://doi.org/10.1080/10942912.2019.1666137

Nichols, D., Cahoon, N., Trakhtenberg, E. M., Pham, L., Mehta, A., Belanger, A., Kanigan, T., Lewis, K., & Epstein, S. S. (2010). Use of ichip for high-throughput in situ cultivation of "uncultivable microbial species▽. Applied and Environmental Microbiology, 76(8), 2445–2450. https://doi.org/10.1128/AEM.01754-09

O’Callaghan, A., & van Sinderen, D. (2016). Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Frontiers in Microbiology, 7. https://doi.org/10.3389/fmicb.2016.00925

Okumura, R., & Takeda, K. (2018). Maintenance of intestinal homeostasis by mucosal barriers. Inflammation and Regeneration, 38(1), 5. https://doi.org/10.1186/s41232-018-0063-z

O’Mahony, S. M., Clarke, G., Borre, Y. E., Dinan, T. G., & Cryan, J. F. (2015). Serotonin, tryptophan metabolism and the brain-gut-microbiome axis. Behavioural Brain Research, 277, 32–48. https://doi.org/10.1016/J.BBR.2014.07.027

Osborne, C. A. (2014). Terminal Restriction Fragment Length Polymorphism (T-RFLP) Profiling of Bacterial 16S rRNA Genes (pp. 57–69). https://doi.org/10.1007/978-1-62703-712-9_5

Otaru, N., Ye, K., Mujezinovic, D., Berchtold, L., Constancias, F., Cornejo, F. A., Krzystek, A., de Wouters, T., Braegger, C., Lacroix, C., & Pugin, B. (2021). GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance. Frontiers in Microbiology, 12. https://doi.org/10.3389/FMICB.2021.656895

Özoğul, F. (2004). Production of biogenic amines by Morganella morganii, Klebsíella pneumoniae and Hafnia alvei using a rapid HPLC method. European Food Research and Technology, 219(5), 465–469. https://doi.org/10.1007/S00217-004-0988-0/TABLES/3

Özoǧul, F., Kuley, E., Özoǧul, Y., & Özoǧul, I. (2012). The Function of Lactic Acid Bacteria on Biogenic Amines Production by Food-Borne Pathogens in Arginine Decarboxylase Broth. Food Science and Technology Research, 18(6), 795–804. https://doi.org/10.3136/FSTR.18.795

PERCIACCANTE, A., & DONELL, S. T. (2022). Microbiome: an old history of a new paradigm. Minerva Gastroenterology, 67(4). https://doi.org/10.23736/S2724-5985.21.02905-3

Perler, B. K., Ungaro, R., Baird, G., Mallette, M., Bright, R., Shah, S., Shapiro, J., & Sands, B. E. (2019). Presenting symptoms in inflammatory bowel disease: descriptive analysis of a community-based inception cohort. BMC Gastroenterology, 19(1), 47. https://doi.org/10.1186/s12876-019-0963-7

Peter, A., Jacob, D. J., Logan, J. A., & Link, C. (2014). The Making of the Microbial Body. Strategic Management Journal, 35(1), 1–23.

PICARD, C., FIORAMONTI, J., FRANCOIS, A., ROBINSON, T., NEANT, F., & MATUCHANSKY, C. (2005). Review article: bifidobacteria as probiotic agents - physiological effects and clinical benefits. Alimentary Pharmacology and Therapeutics, 22(6), 495–512. https://doi.org/10.1111/j.1365-2036.2005.02615.x

Pigeyre, M., Yazdi, F. T., Kaur, Y., & Meyre, D. (2016). Recent progress in genetics, epigenetics and metagenomics unveils the pathophysiology of human obesity. Clinical Science, 130(12), 943–986. https://doi.org/10.1042/CS20160136

Pinto, T. C. A., Costa, N. S., Castro, L. F. S., Ribeiro, R. L., Botelho, A. C. N., Neves, F. P. G., Peralta, J. M., & Teixeira, L. M. (2017). Potential of MALDI-TOF MS as an alternative approach for capsular typing Streptococcus pneumoniae isolates. Scientific Reports, 7(December 2016), 1–5. https://doi.org/10.1038/srep45572

Priya, S., Burns, M. B., Ward, T., Mars, R. A. T., Adamowicz, B., Lock, E. F., Kashyap, P. C., Knights, D., & Blekhman, R. (2022). Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration. Nature Microbiology, 7(6), 780–795. https://doi.org/10.1038/s41564-022-01121-z

Putignani, L., Del Chierico, F., Petrucca, A., Vernocchi, P., & Dallapiccola, B. (2014). The human gut microbiota: a dynamic interplay with the host from birth to senescence settled during childhood. Pediatric Research, 76(1), 2–10. https://doi.org/10.1038/pr.2014.49

Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D. R., Li, J., Xu, J., Li, S., Li, D., Cao, J., Wang, B., Liang, H., Zheng, H., … Zoetendal, E. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), 59–65. https://doi.org/10.1038/nature08821

Quercia, S., Candela, M., Giuliani, C., Turroni, S., Luiselli, D., Rampelli, S., Brigidi, P., Franceschi, C., Bacalini, M. G., Garagnani, P., & Pirazzini, C. (2014). From lifetime to evolution: timescales of human gut microbiota adaptation. Frontiers in Microbiology, 5. https://doi.org/10.3389/fmicb.2014.00587

Quillin, S. J., Tran, P., & Prindle, A. (2021). Potential Roles for Gamma-Aminobutyric Acid Signaling in Bacterial Communities. Bioelectricity, 3(2), 120–125. https://doi.org/10.1089/BIOE.2021.0012

Raman, R., Thomas, R. G., Weiner, M. W., Jack, C. R., Ernstrom, K., Aisen, P. S., Tariot, P. N., & Quinn, J. F. (2005). Diversity of the Human Intestinal Microbial Flora. Science, 308(5728), 1635–1638.

Ramirez, J., Guarner, F., Bustos Fernandez, L., Maruy, A., Sdepanian, V. L., & Cohen, H. (2020). Antibiotics as Major Disruptors of Gut Microbiota. Frontiers in Cellular and Infection Microbiology, 10. https://doi.org/10.3389/fcimb.2020.572912

Ranjbar, J., Geramizadeh, B., Bagheri Lankarani, K., Jowkar, Z., Mirzai, M., & Moazamian, E. (2022). Is the Presence of Helicobacter Pylori in the Colonic Mucosa, Provocative of Activity in Ulcerative Colitis? Clinical Pathology, 15, 2632010X2210966. https://doi.org/10.1177/2632010X221096660

Ren, S., Hui, Y., Obelitz-Ryom, K., Brandt, A. B., Kot, W., Nielsen, D. S., Thymann, T., Sangild, P. T., & Nguyen, D. N. (2018). Neonatal gut and immune maturation is determined more by postnatal age than by postconceptional age in moderately preterm pigs. American Journal of Physiology-Gastrointestinal and Liver Physiology, 315(5), G855–G867. https://doi.org/10.1152/ajpgi.00169.2018

Rhodes, A. N. (1998). Identification of bacterial isolates obtained from intestinal contents associated with 12,000-year-old mastodon remains. Applied Environmental Microbiology, .651-658.

Rich, B. E., Jackson, J. C., de Ora, L. O., Long, Z. G., Uyeda, K. S., & Bess, E. N. (2022). Alternative pathway for dopamine production by acetogenic gut bacteria that O‐Demethylate 3‐Methoxytyramine, a metabolite of catechol O‐Methyltransferase. Journal of Applied Microbiology, 133(3), 1697. https://doi.org/10.1111/JAM.15682

Riddle, M. S., & Connor, B. A. (2016). The Traveling Microbiome. Current Infectious Disease Reports, 18(9). https://doi.org/10.1007/s11908-016-0536-7

Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G. A. D., Gasbarrini, A., & Mele, M. C. (2019a). What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms, 7(1). https://doi.org/10.3390/MICROORGANISMS7010014

Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G., Gasbarrini, A., & Mele, M. (2019b). What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms, 7(1), 14. https://doi.org/10.3390/microorganisms7010014

Rowland, I., Gibson, G., Heinken, A., Scott, K., Swann, J., Thiele, I., & Tuohy, K. (2018). Gut microbiota functions: metabolism of nutrients and other food components. European Journal of Nutrition, 57(1), 1–24. https://doi.org/10.1007/s00394-017-1445-8

Rutayisire, E., Huang, K., Liu, Y., & Tao, F. (2016). The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants’ life: a systematic review. BMC Gastroenterology, 16(1), 86. https://doi.org/10.1186/s12876-016-0498-0

Salim, F., Mizutani, S., Zolfo, M., & Yamada, T. (2023). Recent advances of machine learning applications in human gut microbiota study: from observational analysis toward causal inference and clinical intervention. Current Opinion in Biotechnology, 79, 102884. https://doi.org/10.1016/j.copbio.2022.102884

Salipante, S. J., Kawashima, T., Rosenthal, C., Hoogestraat, D. R., Cummings, L. A., Sengupta, D. J., Harkins, T. T., Cookson, B. T., & Hoffman, N. G. (2014). Performance comparison of Illumina and Ion Torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling. Applied and Environmental Microbiology, 80(24), 7583–7591. https://doi.org/10.1128/AEM.02206-14

Salvi, P. S., & Cowles, R. A. (2021). Butyrate and the Intestinal Epithelium: Modulation of Proliferation and Inflammation in Homeostasis and Disease. Cells, 10(7), 1775. https://doi.org/10.3390/cells10071775

Sánchez, E., Donat, E., Ribes-Koninckx, C., Fernández-Murga, M. L., & Sanz, Y. (2013). Duodenal-Mucosal Bacteria Associated with Celiac Disease in Children. Applied and Environmental Microbiology, 79(18), 5472–5479. https://doi.org/10.1128/AEM.00869-13

Sanschagrin, S., & Yergeau, E. (2014). Next-generation sequencing of 16S ribosomal RNA gene amplicons. Journal of Visualized Experiments, 90, 1–7. https://doi.org/10.3791/51709

Saturio, S., Nogacka, A. M., Alvarado-Jasso, G. M., Salazar, N., de los Reyes-Gavilán, C. G., Gueimonde, M., & Arboleya, S. (2021). Role of Bifidobacteria on Infant Health. Microorganisms, 9(12), 2415. https://doi.org/10.3390/microorganisms9122415

Scardaci, R., Bietto, F., Racine, P.-J., Boukerb, A. M., Lesouhaitier, O., Feuilloley, M. G. J., Scutera, S., Musso, T., Connil, N., & Pessione, E. (2022). Norepinephrine and Serotonin Can Modulate the Behavior of the Probiotic Enterococcus faecium NCIMB10415 towards the Host: Is a Putative Surface Sensor Involved? Microorganisms, 10(3). https://doi.org/10.3390/microorganisms10030487

Scardaci, R., Varese, F., Manfredi, M., Marengo, E., Mazzoli, R., & Pessione, E. (2021). Enterococcus faecium NCIMB10415 responds to norepinephrine by altering protein profiles and phenotypic characters. Journal of Proteomics, 231. https://doi.org/10.1016/J.JPROT.2020.104003

Schoeler, M., & Caesar, R. (2019). Dietary lipids, gut microbiota and lipid metabolism. Reviews in Endocrine and Metabolic Disorders, 20(4), 461–472. https://doi.org/10.1007/s11154-019-09512-0

Scholz, M., Ward, D. V., Pasolli, E., Tolio, T., Zolfo, M., Asnicar, F., Truong, D. T., Tett, A., Morrow, A. L., & Segata, N. (2016). Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nature Methods, 13(5), 435–438. https://doi.org/10.1038/nmeth.3802

Sekirov, I., Russell, S. L., Antunes, L. C. M., & Finlay, B. B. (2010). Gut Microbiota in Health and Disease. Physiological Reviews, 90(3), 859–904. https://doi.org/10.1152/physrev.00045.2009

Selma-Royo, M., Calvo Lerma, J., Cortés-Macías, E., & Collado, M. C. (2021). Human milk microbiome: From actual knowledge to future perspective. Seminars in Perinatology, 45(6), 151450. https://doi.org/10.1016/j.semperi.2021.151450

Seng, P., Abat, C., Rolain, J. M., Colson, P., Lagier, J. C., Gouriet, F., Fournier, P. E., Drancourt, M., Scola, B. La, & Raoult, D. (2013). Identification of rare pathogenic bacteria in a clinical microbiology laboratory: Impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry. Journal of Clinical Microbiology, 51(7), 2182–2194. https://doi.org/10.1128/JCM.00492-13

Seng, P., Drancourt, M., Gouriet, F., Scola, B. La, Fournier, P. E., Rolain, J. M., & Raoult, D. (2009). Ongoing revolution in bacteriology: Routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clinical Infectious Diseases, 49(4), 543–551. https://doi.org/10.1086/600885

Shamir, R. (2016). The Benefits of Breast Feeding (pp. 67–76). https://doi.org/10.1159/000442724

Shankar, V., Hamilton, M. J., Khoruts, A., Kilburn, A., Unno, T., Paliy, O., & Sadowsky, M. J. (2014). Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation. Microbiome, 2(1), 1–10. https://doi.org/10.1186/2049-2618-2-13

Shin, H., Pei, Z., Martinez, K. A., Rivera-Vinas, J. I., Mendez, K., Cavallin, H., & Dominguez-Bello, M. G. (2015). The first microbial environment of infants born by C-section: the operating room microbes. Microbiome, 3(1), 59. https://doi.org/10.1186/s40168-015-0126-1

Shishov, V. A., Kirovskaya, T. A., Kudrin, V. S., & Oleskin, A. V. (2009). Amine neuromediators, their precursors, and oxidation products in the culture of Escherichia coli k-12. Applied Biochemistry and Microbiology, 45(5), 494–497. https://doi.org/10.1134/S0003683809050068/METRICS

Siezen, R. J., & Kleerebezem, M. (2011). The human gut microbiome: are we our enterotypes? Microbial Biotechnology, 4(5), 550. https://doi.org/10.1111/J.1751-7915.2011.00290.X

Siezen RJ, K. M. (2011). The human gut microbiome: are we our enterotypes? Microbial Biotechnology, 550–553.

Sinclair, L., Osman, O. A., Bertilsson, S., & Eiler, A. (2015). Microbial community composition and diversity via 16S rRNA gene amplicons: Evaluating the illumina platform. PLoS ONE, 10(2), 1–18. https://doi.org/10.1371/journal.pone.0116955

Singh, J., Kumar, M., Sharma, A., Pandey, G., Chae, K., & Lee, S. (2016). Genomic Techniques Used to Investigate the Human Gut Microbiota. Intech, 11(tourism), 13.

Sinha, R., Sahoo, N. R., Kumar, P., Qureshi, S., Kumar, A., Ravikumar, G. V. P. P. S., & Bhushan, B. (2018). Comparative jejunal expression of MUC 13 in Indian native pigs differentially adhesive to diarrhoeagenic E. coli. Journal of Applied Animal Research, 46(1), 107–111. https://doi.org/10.1080/09712119.2016.1267009

Sokol H. (2019). Définition et rôles du microbiote intestinal [Definition and roles of the gut microbiota]. . La Revue Du Praticien, 69(7).

Sokol, H., & Seksik, P. (2010). The intestinal microbiota in inflammatory bowel diseases: Time to connect with the host. Current Opinion in Gastroenterology, 26(4), 327–331. https://doi.org/10.1097/MOG.0b013e328339536b

Stasi, C., Sadalla, S., & Milani, S. (2019). The Relationship Between the Serotonin Metabolism, Gut-Microbiota and the Gut-Brain Axis. Current Drug Metabolism, 20(8), 646–655. https://doi.org/10.2174/1389200220666190725115503

Stinson, L. F., Sindi, A. S. M., Cheema, A. S., Lai, C. T., Mühlhäusler, B. S., Wlodek, M. E., Payne, M. S., & Geddes, D. T. (2021). The human milk microbiome: who, what, when, where, why, and how? Nutrition Reviews, 79(5), 529–543. https://doi.org/10.1093/nutrit/nuaa029

Stojanov, S., Berlec, A., & Štrukelj, B. (2020). The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio in the Treatment of Obesity and Inflammatory Bowel disease. Microorganisms, 8(11), 1715. https://doi.org/10.3390/microorganisms8111715

Stokowa-Sołtys, K., Wojtkowiak, K., & Jagiełło, K. (2021). Fusobacterium nucleatum – Friend or foe? Journal of Inorganic Biochemistry, 224, 111586. https://doi.org/10.1016/j.jinorgbio.2021.111586

Strandwitz, P. (2018). Neurotransmitter modulation by the gut microbiota. Brain Research, 1693(Pt B), 128–133. https://doi.org/10.1016/J.BRAINRES.2018.03.015

Strandwitz, P., Kim, K. H., Terekhova, D., Liu, J. K., Sharma, A., Levering, J., McDonald, D., Dietrich, D., Ramadhar, T. R., Lekbua, A., Mroue, N., Liston, C., Stewart, E. J., Dubin, M. J., Zengler, K., Knight, R., Gilbert, J. A., Clardy, J., & Lewis, K. (2019). GABA-modulating bacteria of the human gut microbiota. Nature Microbiology, 4(3), 396–403. https://doi.org/10.1038/S41564-018-0307-3

Suau, A. (1999). Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol., 4799–4807.

Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., Rasmussen, S., Brunak, S., Pedersen, O., Guarner, F., De Vos, W. M., Wang, J., Li, J., Doré, J., Dusko Ehrlich, S., … Bork, P. (2013). Metagenomic species profiling using universal phylogenetic marker genes. Nature Methods, 10(12), 1196–1199. https://doi.org/10.1038/nmeth.2693

Surwase, S. N., & Jadhav, J. P. (2011). Bioconversion of L-tyrosine to L-DOPA by a novel bacterium Bacillus sp. JPJ. Amino Acids, 41(2), 495–506. https://doi.org/10.1007/S00726-010-0768-Z

Swidsinski, A., Loening-Baucke, V., Vaneechoutte, M., & Doerffel, Y. (2008). Active Crohn’s disease and ulcerative colitis can be specifically diagnosed and monitored based on the biostructure of the fecal flora. Inflammatory Bowel Diseases, 14(2), 147–161. https://doi.org/10.1002/ibd.20330

Tang, W. H. W., Kitai, T., & Hazen, S. L. (2017). Gut Microbiota in Cardiovascular Health and Disease. Circulation Research, 120(7), 1183–1196. https://doi.org/10.1161/CIRCRESAHA.117.309715

Tannock, G. W. (2001). Molecular assessment of intestinal microflora. American Journal of Clinical Nutrition, 73(2 SUPPL.), 410–414. https://doi.org/10.1093/ajcn/73.2.410s

Thoeringer, C. K., Erhardt, A., Sillaber, I., Mueller, M. B., Ohl, F., Holsboer, F., & Keck, M. E. (2010). Long-term anxiolytic and antidepressant-like behavioural effects of tiagabine, a selective GABA transporter-1 (GAT-1) inhibitor, coincide with a decrease in HPA system activity in C57BL/6 mice. Journal of Psychopharmacology, 24(5), 733–743. https://doi.org/10.1177/0269881109103091

Thomas, T., Gilbert, J., & Meyer, F. (2014). Metagenomics: A guide from sampling to data analysis. The Role of Bioinformatics in Agriculture, Figure 1, 357–383. https://doi.org/10.1201/b16568

Thrash, J. C. (2019). Culturing the Uncultured: Risk versus Reward. MSystems, 4(3). https://doi.org/10.1128/MSYSTEMS.00130-19

Thursby, E., & Juge, N. (2017). Introduction to the human gut microbiota. Biochemical Journal, 474(11), 1823–1836. https://doi.org/10.1042/BCJ20160510

Tilg, H., & Kaser, A. (2011a). Gut microbiome, obesity, and metabolic dysfunction. Journal of Clinical Investigation, 121(6), 2126–2132. https://doi.org/10.1172/JCI58109

Tilg, H., & Kaser, A. (2011b). Gut microbiome, obesity, and metabolic dysfunction. The Journal of Clinical Investigation, 121(6), 2126–2132. https://doi.org/10.1172/JCI58109

Tringe, S. G., Von Mering, C., Kobayashi, A., Salamov, A. A., Chen, K., Chang, H. W., Podar, M., Short, J. M., Mathur, E. J., Detter, J. C., Bork, P., Hugenholtz, P., & Rubin, E. M. (2005). Comparative metagenomics of microbial communities. Science, 308(5721), 554–557. https://doi.org/10.1126/science.1107851

Tsoi, H., Chu, E. S. H., Zhang, X., Sheng, J., Nakatsu, G., Ng, S. C., Chan, A. W. H., Chan, F. K. L., Sung, J. J. Y., & Yu, J. (2017). Peptostreptococcus anaerobius Induces Intracellular Cholesterol Biosynthesis in Colon Cells to Induce Proliferation and Causes Dysplasia in Mice. Gastroenterology, 152(6), 1419-1433.e5. https://doi.org/10.1053/j.gastro.2017.01.009

Tsukuda, N., Yahagi, K., Hara, T., Watanabe, Y., Matsumoto, H., Mori, H., Higashi, K., Tsuji, H., Matsumoto, S., Kurokawa, K., & Matsuki, T. (2021). Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life. The ISME Journal, 15(9), 2574–2590. https://doi.org/10.1038/s41396-021-00937-7

Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., & Gordon, J. I. (2009). The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice. Science Translational Medicine, 1(6). https://doi.org/10.1126/scitranslmed.3000322

Turpin, W., Goethel, A., Bedrani, L., & Croitoru, M. K. (2018). Determinants of IBD Heritability: Genes, Bugs, and More. Inflammatory Bowel Diseases, 24(6), 1133–1148. https://doi.org/10.1093/ibd/izy085

Uhlig, H. H., & Powrie, F. (2018). Translating Immunology into Therapeutic Concepts for Inflammatory Bowel Disease. Annual Review of Immunology, 36(1), 755–781. https://doi.org/10.1146/annurev-immunol-042617-053055

Underwood, M. A., Gaerlan, S., De Leoz, M. L. A., Dimapasoc, L., Kalanetra, K. M., Lemay, D. G., German, J. B., Mills, D. A., & Lebrilla, C. B. (2015). Human milk oligosaccharides in premature infants: absorption, excretion, and influence on the intestinal microbiota. Pediatric Research, 78(6), 670–677. https://doi.org/10.1038/pr.2015.162

Valdes, A. M., Walter, J., Segal, E., & Spector, T. D. (2018). Role of the gut microbiota in nutrition and health. BMJ, k2179. https://doi.org/10.1136/bmj.k2179

Valles-Colomer, M., Falony, G., Darzi, Y., Tigchelaar, E. F., Wang, J., Tito, R. Y., Schiweck, C., Kurilshikov, A., Joossens, M., Wijmenga, C., Claes, S., Van Oudenhove, L., Zhernakova, A., Vieira-Silva, S., & Raes, J. (2019). The neuroactive potential of the human gut microbiota in quality of life and depression. Nature Microbiology, 4(4), 623–632. https://doi.org/10.1038/S41564-018-0337-X

Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., Fouts, D. E., Levy, S., Knap, A. H., Lomas, M. W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., … Smith, H. O. (2004). Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science, 304(5667), 66–74. https://doi.org/10.1126/science.1093857

Verhaar, B. J. H., Prodan, A., Nieuwdorp, M., & Muller, M. (2020). Gut Microbiota in Hypertension and Atherosclerosis: A Review. Nutrients, 12(10), 2982. https://doi.org/10.3390/nu12102982

Vester-Andersen, M. K., Mirsepasi-Lauridsen, H. C., Prosberg, M. V., Mortensen, C. O., Träger, C., Skovsen, K., Thorkilgaard, T., Nøjgaard, C., Vind, I., Krogfelt, K. A., Sørensen, N., Bendtsen, F., & Petersen, A. M. (2019). Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis. Scientific Reports 2019 9:1, 9(1), 1–10. https://doi.org/10.1038/s41598-019-49833-3

Viglasky, V. (2013). Polyacrylamide Temperature Gradient Gel Electrophoresis (pp. 159–171). https://doi.org/10.1007/978-1-62703-565-1_10

Volsky, S. K., Shalitin, S., Fridman, E., Yackobovitch-Gavan, M., Lazar, L., Bello, R., Oron, T., Tenenbaum, A., Vries, L. de, & Lebenthal, Y. (2021). Dyslipidemia and cardiovascular disease risk factors in patients with type 1 diabetes: A single-center experience. World Journal of Diabetes, 12(1), 56–68. https://doi.org/10.4239/wjd.v12.i1.56

Wagner, J., Coupland, P., Browne, H. P., Lawley, T. D., Francis, S. C., & Parkhill, J. (2016). Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification. BMC Microbiology, 16(1), 1–17. https://doi.org/10.1186/s12866-016-0891-4

Wall, R., Hussey, S. G., Ryan, C. A., O’Neill, M., Fitzgerald, G., Stanton, C., & Ross, R. P. (2008). Presence of two Lactobacillus and Bifidobacterium probiotic strains in the neonatal ileum. The ISME Journal, 2(1), 83–91. https://doi.org/10.1038/ismej.2007.69

Walter, J. (2008). Ecological Role of Lactobacilli in the Gastrointestinal Tract: Implications for Fundamental and Biomedical Research. Applied and Environmental Microbiology, 74(16), 4985–4996. https://doi.org/10.1128/AEM.00753-08

Wang, J., Dong, P., Zheng, S., Mai, Y., Ding, J., Pan, P., Tang, L., Wan, Y., & Liang, H. (2023). Advances in gut microbiome in metabonomics perspective: based on bibliometrics methods and visualization analysis. Frontiers in Cellular and Infection Microbiology, 13. https://doi.org/10.3389/fcimb.2023.1196967

Witkowski, M., Weeks, T. L., & Hazen, S. L. (2020). Gut Microbiota and Cardiovascular Disease. Circulation Research, 127(4), 553–570. https://doi.org/10.1161/CIRCRESAHA.120.316242

Wooley, J. C., Godzik, A., & Friedberg, I. (2010). A primer on metagenomics. PLoS Computational Biology, 6(2). https://doi.org/10.1371/journal.pcbi.1000667

Wu, G. D., Lewis, J. D., Hoffmann, C., Chen, Y.-Y., Knight, R., Bittinger, K., Hwang, J., Chen, J., Berkowsky, R., Nessel, L., Li, H., & Bushman, F. D. (2010). Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiology, 10(1), 206. https://doi.org/10.1186/1471-2180-10-206

Wu, H., Tremaroli, V., Schmidt, C., Lundqvist, A., Olsson, L. M., Krämer, M., Gummesson, A., Perkins, R., Bergström, G., & Bäckhed, F. (2020). The Gut Microbiota in Prediabetes and Diabetes: A Population-Based Cross-Sectional Study. Cell Metabolism, 32(3), 379-390.e3. https://doi.org/10.1016/j.cmet.2020.06.011

Xi, Y., & Xu, P.-F. (2021). Diabetes and gut microbiota. World Journal of Diabetes, 12(10), 1693. https://doi.org/10.4239/WJD.V12.I10.1693

Xiao, Y., Zhai, Q., Zhang, H., Chen, W., & Hill, C. (2021a). Gut Colonization Mechanisms of Lactobacillus and Bifidobacterium : An Argument for Personalized Designs. Annual Review of Food Science and Technology, 12(1), 213–233. https://doi.org/10.1146/annurev-food-061120-014739

Xiao, Y., Zhai, Q., Zhang,

Downloads

Published

28-12-2024

How to Cite

Rashid, M., Sinha , D., Usama, M., Badam, M., Idrees, M., Noureen , S., … Ghazanfar, S. (2024). In-Depth Exploration of Human Gut Microbiota: A Review: Human Gut Microbiota Attributes. Kashmir Journal of Science, 3(04). Retrieved from https://kjs.org.pk/index.php/kjs/article/view/88

Similar Articles

You may also start an advanced similarity search for this article.